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CHECK report for CellTrails on merida1

This page was generated on 2020-04-15 12:47:38 -0400 (Wed, 15 Apr 2020).

Package 249/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CellTrails 1.4.0
Daniel Ellwanger
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/CellTrails
Branch: RELEASE_3_10
Last Commit: 71d24e0
Last Changed Date: 2019-10-29 13:11:14 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CellTrails
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CellTrails.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CellTrails_1.4.0.tar.gz
StartedAt: 2020-04-15 01:02:50 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 01:07:41 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 291.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: CellTrails.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CellTrails.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CellTrails_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/CellTrails.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CellTrails/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CellTrails’ version ‘1.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CellTrails’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike' is deprecated.
  Warning: 'isSpike' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
        user system elapsed
plotMap 9.88  0.677  10.652
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/CellTrails.Rcheck/00check.log’
for details.



Installation output

CellTrails.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CellTrails
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘CellTrails’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CellTrails)

Tests output

CellTrails.Rcheck/tests/runTests.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("CellTrails")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Computing adjacency matrix ...
Computing spectral embedding ...
Calculating approximation of CellTrails manifold for 2D visualization...
Used tSNE perplexity: 30
Initialized 20 clusters with a minimum size of 1 samples each.
Performing post-hoc test ...
Found 5 states.
Calculating layout of state trajectory graph component 1...
Computing adjacency matrix ...
Computing spectral embedding ...
Calculating approximation of CellTrails manifold for 2D visualization...
Used tSNE perplexity: 30
Initialized 20 clusters with a minimum size of 1 samples each.
Performing post-hoc test ...
Found 5 states.
Calculating layout of state trajectory graph component 1...
Calculating layout of state trajectory graph component 2...
Calculating layout of state trajectory graph component 3...
Calculating layout of state trajectory graph component 4...
Calculating layout of state trajectory graph component 5...
Calculating layout of state trajectory graph component 1...
Computing adjacency matrix ...
Computing spectral embedding ...
Computing adjacency matrix ...
Computing spectral embedding ...
Calculating approximation of CellTrails manifold for 2D visualization...
Used tSNE perplexity: 30
Computing adjacency matrix ...
Computing spectral embedding ...
Calculating approximation of CellTrails manifold for 2D visualization...
Used tSNE perplexity: 30
Initialized 20 clusters with a minimum size of 1 samples each.
Performing post-hoc test ...
Found 1 states.
Initialized 20 clusters with a minimum size of 1 samples each.
Performing post-hoc test ...
Found 1 states.
Initialized 0 clusters with a minimum size of 1000 samples each.
Initialized 20 clusters with a minimum size of 1 samples each.
Performing post-hoc test ...
Found 20 states.
Initialized 20 clusters with a minimum size of 1 samples each.
Performing post-hoc test ...
Found 1 states.
Initialized 20 clusters with a minimum size of 1 samples each.
Performing post-hoc test ...
Found 19 states.
Initialized 20 clusters with a minimum size of 1 samples each.
Performing post-hoc test ...
Found 5 states.
Initialized 20 clusters with a minimum size of 1 samples each.
Performing post-hoc test ...
Found 5 states.
Computing adjacency matrix ...
Computing spectral embedding ...
Calculating approximation of CellTrails manifold for 2D visualization...
Used tSNE perplexity: 30
Initialized 20 clusters with a minimum size of 1 samples each.
Performing post-hoc test ...
Found 5 states.
Calculating layout of state trajectory graph component 1...
Computing adjacency matrix ...
Computing spectral embedding ...
Calculating approximation of CellTrails manifold for 2D visualization...
Used tSNE perplexity: 30
Initialized 20 clusters with a minimum size of 1 samples each.
Performing post-hoc test ...
Found 5 states.
Calculating layout of state trajectory graph component 1...
Computing adjacency matrix ...
Computing spectral embedding ...
Calculating approximation of CellTrails manifold for 2D visualization...
Used tSNE perplexity: 30
Initialized 20 clusters with a minimum size of 1 samples each.
Performing post-hoc test ...
Found 5 states.
Calculating layout of state trajectory graph component 1...
Calculating 2D approximation of CellTrails manifold...
Calculating layout of state trajectory graph component 1...
Calculating layout of state trajectory graph component 2...
Calculating layout of state trajectory graph ...
Computing adjacency matrix ...
Computing spectral embedding ...
Calculating approximation of CellTrails manifold for 2D visualization...
Used tSNE perplexity: 30
Initialized 20 clusters with a minimum size of 1 samples each.
Performing post-hoc test ...
Found 5 states.
Calculating layout of state trajectory graph component 1...


RUNIT TEST PROTOCOL -- Wed Apr 15 01:07:34 2020 
*********************************************** 
Number of test functions: 18 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
CellTrails RUnit Tests - 18 test functions, 0 errors, 0 failures
Number of test functions: 18 
Number of errors: 0 
Number of failures: 0 
There were 32 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
 47.014   1.144  49.126 

Example timings

CellTrails.Rcheck/CellTrails-Ex.timings

nameusersystemelapsed
addTrail0.7450.0460.794
connectStates0.1030.0070.111
contrastTrailExpr0.3350.0130.349
embedSamples0.9030.0310.941
enrichment.test0.0040.0000.003
featureNames-SingleCellExperiment-method0.0210.0050.025
filterTrajFeaturesByCOV3.5150.1383.678
filterTrajFeaturesByDL1.6900.0641.762
filterTrajFeaturesByFF3.9570.1724.152
findSpectrum0.6310.0250.660
findStates1.3270.0221.368
fitDynamic0.1960.0110.216
fitTrajectory0.6310.0160.655
landmarks0.0230.0110.033
latentSpace-set0.5500.0130.621
latentSpace0.0540.0080.062
manifold2D-set0.6450.0100.661
manifold2D0.0590.0090.067
pca0.3390.0110.354
phenoNames0.0190.0070.027
plotDynamic1.1460.0151.171
plotManifold1.1150.0101.139
plotMap 9.880 0.67710.652
plotStateExpression0.8300.0210.875
plotStateSize0.2200.0040.229
plotStateTrajectory1.2410.0081.256
plotTrail0.3750.0040.381
plotTrajectoryFit0.4060.0040.414
read.ygraphml0.0120.0030.015
removeTrail0.0390.0030.042
sampleNames-SingleCellExperiment-method0.0200.0030.022
selectTrajectory0.0180.0030.021
showTrajInfo0.2350.0050.241
simulate_exprs0.0020.0000.001
stateTrajLayout-set0.1770.0030.186
states-set0.0390.0030.042
states0.0180.0030.020
trailNames-set0.0150.0030.019
trailNames0.0100.0030.012
trails0.0340.0020.037
trajComponents0.0110.0020.014
trajFeatureNames-set0.0310.0030.034
trajFeatureNames0.0250.0030.027
trajLayout-set0.5970.0060.609
trajLayout0.0170.0020.019
trajResiduals0.0110.0020.013
trajSampleNames0.0160.0020.018
userLandmarks-set0.5550.0030.560
userLandmarks0.1580.0040.163
write.ygraphml0.0110.0020.013